Molina, who is also a free agent, will not be back with the Blue Jays next season.
Zaun's new deal includes an option for 2009, which could become guaranteed based on performance.
The Blue Jays, who finished second last season in the American League East Division behind the Yankees, originally thought they had signed Rod Barajas to a two-year contract. Barajas, however, decided not to go through with the deal and switched agents, forcing Toronto General manager J.P. Ricciardi to negotiate a new deal with Zaun.
"Zaunie was our first choice all along. It just hit a snag there at one point. I called him [Monday night] and said 'Zaunie, if you want to be a Blue Jay we got to make it happen now,'" Ricciardi told the Associated Press during a team press conference Tuesday.
The Blue Jays wanted to finalize their catching situation so they could focus on acquiring an infielder and a starting pitcher at next week's baseball winter meetings in Orlando, Fla.
He's expected to team with backup Jason Phillips, while prospect Curtis Thigpen develops.
Zaun, who helped the Florida Marlins win the 1997 World Series against the Cleveland Indians, hit .272 (79 for 290) with a career-high 12 home runs and 40 runs batted in during 99 games last season. He also played for the Baltimore Orioles, Texas Rangers, Kansas City Royals, Houston Astros and Colorado Rockies before joining Toronto in 2004.
In 918 games, the switch-hitting Zaun has a .253 (645 for 2,549) batting average with 62 home runs and 323 RBIs. The former Mission League standout has scored 320 runs and stolen 21 bases in his career.
While Zaun knows his destination, the same can't be said for another former St. Francis star.
Mark Loretta, who played for the Red Sox in 2006, is a free agent. Early reports had the infielder, who started last season for the American League in the All-Star Game, drawing interest from the New York Mets.
Loretta, 35, fared well for the Red Sox, who placed third in the American League East Division last season and failed to qualify for the postseason for the first time since 2002. He batted .285 (181 for 635) with five home runs and 59 RBIs in 155 games played. He finished with 33 doubles while hitting in front of the powerful tandem of David Ortiz and Manny Ramirez.
Loretta also played for the Milwaukee Brewers, Astros and San Diego Padres. He played in the 2004 All-Star Game as a member of the Padres.
CHARLES RICH covers sports. He can be reached at (818) 637-3228 or by e-mail at email@example.com.